In some cases students were given credit for courses that they never even took.
Klarice Williamson is one of about a hundred seniors at Jane Addams High who were told they may not graduate.
She took cosmetology, or "Cos" as some call it, while getting credit for Chemistry.
"That's messing up what I could have learned. I could have learned chemistry," Williamson said.
"They haven't had a chemistry teacher in here since 2009. They didn't have it," said Josephine Bello, Klarice's mother.
Principal Sharron Smalls is now under investigation for the practice known as "double dipping".
"Students have definitely, have classes on their transcripts that they have been given credit for certain subjects that they did not earn," said Stephen Tavano, a teacher at Addams High School.
Veteran math teacher Stephen Tavano is the Teachers Union leader at the school.
"How were teachers talked into doing that, Steve?" Eyewitness News asked.
"Teachers were not. It's the administration's direction," Tavano said.
In a statement Thursday, the Department of Education said, in part, "We are investigating a series of anonymous allegations recently made about the principal and staff. Sadly, this is a school that for years has performed far below citywide averages on critical academic measures, which is why we are considering phasing it out and providing students with better options."
"They should do something about the school. Just put in a whole bunch of new deans, a new principal, everything. Everything is wrong with that school," said Carolina Goez, an Addams High School student.
Principal Smalls has not returned Eyewitness News' call, asking for comment.
"She's been here for what, four or five years already? She still didn't do anything. She's giving kids courses, credit for courses that they never took. Who does that?" Bello said.